X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fclarguments.html;h=88657f8d65c5a80e0bada0b42ab158655c3f9ac8;hb=ab7509436f09413b122dace2ecd6692f6f06d347;hp=9ca64a6d4258a9f0ec246e8e981edf7c2781d27f;hpb=ff4d98fbde57ca9dea2fc607d36d80a00963746d;p=jalview.git

diff --git a/help/html/features/clarguments.html b/help/html/features/clarguments.html
index 9ca64a6..88657f8 100644
--- a/help/html/features/clarguments.html
+++ b/help/html/features/clarguments.html
@@ -30,12 +30,12 @@
  </tr>
 
  <tr> 
- <td><div align="center">-props FILE</div></td>
+ <td><div align="center">-props FILE/URL</div></td>
  <td><div align="left">Use the given Jalview properties file instead 
  of users default.</div></td>
  </tr>
  <tr> 
- <td><div align="center">-features FILE</div></td>
+ <td><div align="center">-features FILE/URL</div></td>
  <td><div align="left"> 
  <p>Use the given file to add sequence features to an alignment. 
  See <a href="featuresFormat.html" target="NEW">Features 
@@ -55,7 +55,7 @@
  </tr>
 	<tr>
 		<td>
-		<div align="center">-annotations FILE</div>
+		<div align="center">-annotations FILE/URL</div>
 		</td>
 		<td>Add precalculated annotations to the alignment. See <a
 			href="annotationsFormat.html" target="NEW">Annotation File</a>
@@ -63,7 +63,7 @@
 	</tr>
 	<tr>
 		<td>
-		<div align="center">-tree FILE</div>
+		<div align="center">-tree FILE/URL</div>
 		<td>
 		<div align="left">Load the given newick format tree file onto
 		the alignment</div>
@@ -117,7 +117,7 @@
 	</tr>
 	<tr>
 		<td>
-		<div align="center">-groovy FILE</div>
+		<div align="center">-groovy FILE/URL</div>
 		<td>
 		<div align="left">Execute groovy script in FILE (where FILE may be 'STDIN' to read from the standard input) after all other
 		arguments have been processed</div>
@@ -125,7 +125,7 @@
 	</tr>
 	<tr>
 	<td>
-		<div align="center">-vdoc VAMSAS DOCUMENT FILE or URL</div>
+		<div align="center">-vdoc VAMSAS DOCUMENT FILE/URL</div>
 		<td>
 		<div align="left">Import the given vamsas document into a new session.<br><em>New in 2.5</em></div>
 		</td>
@@ -139,14 +139,6 @@
 	</tr>
 	<tr>
 		<td>
-		<div align="center">-groovy FILE</div>
-		<td>
-		<div align="left">Execute groovy script in FILE (where FILE may be 'STDIN' to read from the standard input) after all other
-		arguments have been processed</div>
-		</td>
-	</tr>
-	<tr>
-		<td>
 		<div align="center">-fasta FILE</div>
 		</td>